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- W2051250230 abstract "Hybrid all-atom (AA) and coarse-grained (CG) simulation has the possibility of overcoming the limitations of both AA and CG molecular dynamics (MD) simulations. Hybrid AA/CG systems are practicable to simulate microsecond time scale and to get detailed information for molecular structures. Many existing methods for hybrid AA/CG simulations tend to require heavy parameterizations that complicate multiscale simulations. We test a simple scheme for simulating hybrid AA/CG systems using standard AA and CG force fields, together with four small proteins as test cases for the scheme. Our method uses virtual sites for interactions between CG and AA resolution as reported earlier (Rzepiela et al. Phys. Chem. Chem. Phys. 2011, 13, 10437-10448) and we add distance restrained FG water layer to improve the reliability of the hybrid simulation. We observe that the addition of distance restrained FG water layer in the hybrid simulation results in close accord with the structure from the atomistic simulations. However, there are also digressions from correct behaviors that need to be addressed in future developments. We show such various results in detail and discuss the prospects of our scheme." @default.
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- W2051250230 date "2014-01-01" @default.
- W2051250230 modified "2023-10-16" @default.
- W2051250230 title "Simple Method for Hybrid All-Atom and Coarse-Grained Molecular Dynamics Simulations and Its Applications" @default.
- W2051250230 doi "https://doi.org/10.1016/j.bpj.2013.11.2322" @default.
- W2051250230 hasPublicationYear "2014" @default.
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